Cryptic Covid strains found in 13 states, including California, New York

More than 30 extremely mutated, never-before-seen Covid strains are lurking in multiple US states, DailyMail.com can reveal. 

A team of scientists from the University of Missouri has been tracking these so-called ‘cryptic’ variants by testing wastewater samples across the country.

They have detected 32 strains so far in 13 states — including New York, California and Florida — but say these cases are just the ‘tip of the iceberg’.

The viruses are being harbored by people known as ‘long-haulers’, patients who struggle to clear Covid infection for months or even years, giving the virus an unusually long window to mutate.

Dr Marc Johnson, the virologist at Missouri who is leading the research, warned the strains are so mutated they would instantly be classed ‘variants of concern’ if they were to start spreading.

Hover over map to see how many cryptic lineages have been discovered in your state! 

Dr Marc Johnson (pictured), a virologist at the University of Missouri, told DailyMail.com that finding the people harboring cryptic lineages can give a greater understanding of the virus and why is causes ‘long Covid’

‘I assume the cryptic lineages are the tip of the iceberg,’ Dr Johnson said.

‘If there’s this many long-term infections [we have found], how many are we not detecting.’

He believes more resources should be invested in finding these strains, saying: ‘It would be worthwhile to figure out who has the infection and why.’

The scientist is unsure whether the patients shedding the novel variants are contagious or how they have managed to stay infected so long.

Dr Johnson does not think they are infectious. But he warns if the patients continue to harbor the viruses, there is a risk they acquire a mutation that allows them to spread rapidly through the population.

None of the patients carrying a cryptic lineage have been identified, and little is known about each of them.

In a report last year, Dr Johnson’s team wrote that: ‘The simplest explanation for the appearance of cryptic lineages in wastewater is that they are shed by immunosuppressed patients with persistent infections.’

Patients who harbor viruses for exceptionally long periods of time often have weakened immune systems, which means their body struggles to clear the virus.

Many scientists believe the Alpha, Delta and Omicron variants all emerged this way. 

They likely all have some sort of genetic mutation in common that allows the virus to evade their immune system for so long. 

‘I’m guessing there is something similar about these patients but it might not be obvious,’ he said.

He believes that one in every 4million people are harboring one of these strains, or have in the past. This would mean there are about 80 cryptic lineages circualting.

So far, ten have been detected in New York City —  more than double any individual state.

The virologist said that this is because the city is so densely populated that wastewater samples from the big apple include more people than in other areas.

As a result, it is easier to detect these strains in the Big Apple than anywhere else. 

Four have been detected in California, and one to three lineages have been found 11 other scattered states.

These include: Colorado, Florida, Kentucky, Missouri, Montana, New Jersey, Ohio, Oklahoma, Texas, Virginia and Wisconsin. 

‘I wasn’t looking for them; we just started sequencing things that didn’t match up,’ Dr Johnson said of his first encounters with the lineages.

Wastewater sequencing is a tool used by virologists and public health experts to gather data on the prevalence of different viruses in a local community.

Scientists will gather samples of sewer water and test it to look for different strains.

Because a person will shed the virus in the stool before they suffer symptoms, this type of surveillance can allow public health experts to get ahead of some outbreaks.

One of those strains was found in Central Ohio, where Dr Johnson’s team believes they have found a person who has been infected with the virus for at least two years.

This person regularly commutes between Columbus — the state’s largest city — and Washington Court House, a small town of 15,000 40 miles southwest.

Researchers have found the same cryptic lineage circulating between the two cities since at least March 2021. 

This same lineage has not been detected anywhere else to the scientists’ knowledge. 

This specific pattern likely means the person lives in Washington Court House and commutes to Columbus.

It could be for work, but the patient could also be a student, as Columbus is home to Ohio State University — which has more than 66,000 students.

It is unclear how the person has harbored the virus for so long, but it is likely the virus has mutated within him to cause little complications.

Overall, there are likely only a few thousand people that meet these guidelines, a relatively small group to be sifted through.

In Spring 2022, Dr Johnson found a cryptic strain in Wisconsin. The afflicted person was shedding viral load at an exorbitant rate.

His team tested water in manholes in the area, and managed to track down where the load was coming from.

In late Summer 2022, they linked the strain to a toilet at a specific building, which employed many people who were coming to work each day. One of those employees is carrying the cryptic strain, Dr Johnson believes.

A person in Ohio has been infected with Covid for over two years. Researchers found that they regularly commute from the small city of Washington Court House around 40 miles northeast to Columbus, Ohio. It is likely they live in Washington and work or go to school in Columbus

The man’s Covid strain has evolved significantly differently than existing strains such as the Omicron and Delta variants that the population is familiar with. Pictured: A viral ‘tree’ the shows how different versions of Covid have evolved. Clustered in the center (blue arrow) are familiar variants that have circulated across the world. Within these strains, there are thousands, if not millions, of mutations differentiating them. The unknown Ohio person’s strain (red line) has mutated totally separately, though. It’s viral makeup is greatly different than that of other versions of the virus, and its evolutionary chain is linear — without thousands of branching paths. This indicates that the strain is only circulating in a single person.

The business has agreed to allow Dr Johnson to collect stool samples from some employees to determine which one is carrying the strain.

The typical Covid case lasts for only a few days — and the maximum time someone should expect to be sick is two weeks.

Dr Johnson hopes that finding the people harboring these cases can allow scientists to learn more about the virus itself and whether these cryptic lineages are tied to the phenomenon of ‘long Covid’. 

‘I assume the cryptic lineages are the tip of the iceberg. If there’s this many long term infections then how many more are we not detecting,’ he explained. 

‘It would be worthwhile to figure out who has these infections and why.’

In March 2021, Dr Johnson first encountered a mysterious lineage when sequencing wastewater in Missouri.

His team discovered a strain of Covid they had never seen before. Over a month, they detected 12 samples of a strain with up to six mutations differing from the typically circulating strains.

When expanding their research, scientists would find six unknown lineages circulating in New York City, one in California and a second in Missouri over the coming months.

They would name them ‘cryptic lineages’, and went on a search to determine where they were coming from.

At first, the virologists thought the strains were circulating in animals. Rats were a simple answer because of how many are infesting New York City’s sewers.

However, some strains showed RNA that was inconsistent with rodent infection and the mutations the viruses picked up were human ‘immune escape mutations’, meaning they would help it evade a person’s immune system.

If rats were hosting the strains, they would not mutate to escape the human immune system.

Patients likely do not know they have Covid. Instead, they are either asymptomatic or suffering symptoms similar to a stomach infection.

These would include diarrhea, nausea, vomiting and other relatively-manageable symptoms.

In many cases the person will still be able to perform daily activities such as going to work or caring for their children.